Simulating Tissues with Oneiric

Introduction

library(oneiric)
library(ggplot2)
library(RColorBrewer)
set.seed(288)

Data

Chaos Parameters

data(oneiric)
str(map_params)

##  num [1:36, 1:6] -1.452 -0.983 1.536 -0.91 2.613 ...
##  - attr(*, "dimnames")=List of 2
##   ..$ : NULL
##   ..$ : chr [1:6] "a" "b" "c" "d" ...

Simulated Territories

sim_ter <- system.file("extdata", package = "oneiric")

Creating New Data sets

Simulate New Territories

circles <- simulate_spatial(n_cells = 6000,
    n_territories = 5,
    n_samples = 12,
    pattern = "circle",
    max_expanse = 0.3)

rods <- simulate_spatial(n_cells = 6000,
    n_territories = 5,
    n_samples = 12,
    pattern = "rod",
    max_width = 0.1,
    max_length = 0.5)

chaos <- simulate_spatial(n_cells = 6000,
    n_samples = 12,
    pattern = "chaos",
    max_expanse = 0.02)

Circular Territories

circles <- do.call("rbind", circles)
circles$Territory <- as.factor(circles$Territory)
g <- ggplot(circles, aes(x = x, y = y, col = Territory)) +
    geom_point(size = 0.5) +
    theme_bw() +
    scale_color_brewer(palette="Spectral") +
    facet_wrap(~sample) +
    guides(colour = guide_legend(
        override.aes = list(size =  5)))
print(g)

Circular Territories

Rod Territories

rods <- do.call("rbind", rods)
rods$Territory <- as.factor(rods$Territory)
g <- ggplot(rods, aes(x = x, y = y, col = Territory)) +
    geom_point(size = 0.5) +
    theme_bw() +
    scale_color_brewer(palette="Spectral") +
    facet_wrap(~sample)+
    guides(colour = guide_legend(
        override.aes = list(size =  5)))
print(g)

Rod Territories

Tinkerbell Map Territories

chaos <- do.call("rbind", chaos)
chaos$Territory <- as.factor(chaos$Territory)
g <- ggplot(chaos, aes(x = x, y = y, col = Territory)) +
    geom_point(size = 0.5) +
    theme_bw() +
    scale_color_brewer(palette="Spectral") +
    facet_wrap(~sample)+
    guides(colour = guide_legend(
        override.aes = list(size =  5)))
print(g)

Tinkerbell Map Territories